Cow Genome update in Tophat
by Aranday-Cortes, Elihu
Hi Galaxy Team,
I'd like to use Tophat but the last version of the cow genome is not listed (BotsTau7). Tha last version is listed is BosTau4 . any chance for an update?
Thanks
Elihu
10 years, 3 months
RV: Subdivide peaks
by Mónica Pérez Alegre
Hi
I´m working with data from tiling array (S.cerevisiae). I need to analyze the distribution of the enrichment signal along the length of all ORFs. So I want subdivide the genomics intervals into 10 segments independent of ORF size. Are there any tools in galaxy for this?
Thanks for the helpful
Regards
☺If you have used the Services of the Genomics Unit of Cabimer, we would be grateful if you would give us a mention in future publications
Mónica Pérez Alegre, PhD
Genomics Unit
CABIMER-CSIC
Edif. CABIMER - Avda. Américo Vespucio s/n
Parque Científico y Tecnológico Cartuja 93
41092 Seville-SPAIN
Tlf: +34 954 467 828
Fax: +34 954 461 664
www.cabimer.es<http://www.cabimer.es/>
http://www.cabimer.es/web/es/unidades-apoyo/genomica
10 years, 3 months
Cleanup script error - guess_dialect_for_url
by rocco.piazza
Hello,
I'm working on a local instance of Galaxy-dist and I just
updated it. Right after the update I tried to run the
cleanup scripts. Unfortunately what I'm getting is the
following error:
# sh delete_datasets.sh -d 0 -r
Traceback (most recent call last):
File "./scripts/cleanup_datasets/cleanup_datasets.py",
line 524, in <module>
if __name__ == "__main__": main()
File "./scripts/cleanup_datasets/cleanup_datasets.py",
line 101, in main
app = CleanupDatasetsApplication( config )
File "./scripts/cleanup_datasets/cleanup_datasets.py",
line 512, in __init__
self.model = galaxy.model.mapping.init(
config.file_path, config.database_connection,
engine_options={}, create_tables=False,
object_store=self.object_store )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1818, in init
load_egg_for_url( url )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1798, in load_egg_for_url
dialect = guess_dialect_for_url( url )
File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1794, in guess_dialect_for_url
return (url.split(':', 1))[0]
AttributeError: 'bool' object has no attribute 'split'
The same error occurs if I try to run other cleanup
scripts, such as the delete_datasets or purge_datasets.
Any idea to solve this issue?
Best regards,
Rocco
10 years, 3 months
How can I sort BAM/SAM file by read names?
by Carlos Borroto
Hi,
I need to sort a BAM file by read names, I was wondering if this is
possible with a tool included in Galaxy?
I know any BAM file produced inside Galaxy will be sorted by
coordinates, but I couldn't find an option to change this to queryname
in any tool. Picard has the tool SortSam[1], perfect for this task,
but it doesn't seem to be included at the moment. Is there any other
option currently included? Are there any plans to include one?
[1]http://picard.sourceforge.net/command-line-overview.shtml#SortSam
Thanks,
Carlos
10 years, 3 months
Reference genomes at local instance of Galaxy
by Yang, Yanming
Hi,
I have just installed a Galaxy instance at my local machine and uploaded some sequence data into it. But, when I tried to use some NGS tools which need reference genome, I found the selection window was empty. I wonder how to get a reference genome data (e.g., hg19) incorporated into the local Galaxy.
Any help will be greatly appreciated. Thanks!
Yanming Yang
10 years, 3 months
Table with gene count reads
by Luciano Cosme
Hi,
I was wondering if there is any tool on Galaxy were I can obtain a table
with how many reads have been mapped to a given sample and to a given gene
(for example, use a Tophat output and use a GFF file to obtain the table).
I am using HTSeq to get it (htseq-count). There is also GenomicRanges and
easyRNASeq packages in bioconductor.
Thank you.
Luciano
10 years, 3 months
problems with color settings in Visualizations
by Mackenzie Gavery
Hi,
I am working with some saved visualizations, and finding that the color
settings are not working today. Specifically, every time I change the color
(in Settings) the result is the feature ends up black regardless of the
color selection. Could you help me with this issue?
Thanks,
Mackenzie
10 years, 3 months
Subdivide peaks
by Mónica Pérez Alegre
Hi
I´m working with data from tiling array (S.cerevisiae). I need to analyze the distribution of the enrichment signal along the length of all ORFs. So I want subdivide the genomics intervals into 10 segments independent of ORF size. Are there any tools in galaxy for this?
Thanks for the helpful
Regards
☺If you have used the Services of the Genomics Unit of Cabimer, we would be grateful if you would give us a mention in future publications
Mónica Pérez Alegre, PhD
Genomics Unit
CABIMER-CSIC
Edif. CABIMER - Avda. Américo Vespucio s/n
Parque Científico y Tecnológico Cartuja 93
41092 Seville-SPAIN
Tlf: +34 954 467 828
Fax: +34 954 461 664
www.cabimer.es<http://www.cabimer.es/>
http://www.cabimer.es/web/es/unidades-apoyo/genomica
10 years, 3 months
"Job is waiting to run"
by Shisheng Li
Dear Sir/Madam,
I am a registered user of the public Galaxy Server (main). Any job I
submitted today is labeled as "Job is waiting to run" forever. The total
volume of my files is 249 mb, which is far below the quota limit of 250 gb,
and I am trying to run less than 8 jobs. Could you please let me know the
possible reasons?
Sincerely,
Shisheng
10 years, 3 months
